Psst! I've posted some details about my notebook setup here.

Shell pipelines in Python

The UNIX shell is an indispensible tool for project organization and data management in bioinformatics. I spend a lot of time in the shell, and having picked up on a lot of time-saving techniques over the years it might just be my favorite computing environment.

The shell has its limitations, however. Piping, the very feature that gives the shell its …

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Filter stderr while piping in UNIX

Permalink: 2015-12-14 by Daniel S. Standage in blog tags: shell

Nifty trick for filtering stderr in the middle of a shell pipeline.

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Consortium authors in EndNote

Today I was reformatting a manuscript and changing from a numbered citation style to an author/date citation style. In doing so, I found some issues with my EndNote references library that had gone unnoticed before since they were tucked away in the reference list. One of the issues involved citation of a paper with a single consortium author, designated …

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New lab notebook setup: my motivation

Permalink: 2015-11-17 by Daniel S. Standage in blog tags: meta

My first research blog was a self-hosted Wordpress blog run from an Ubuntu server in our lab. I was initially enamored by the supposed control and flexibility this gave me, but when I changed institutions a year or so later I was not quite as enamored with the work that went into migrating the content, nor the time I spent …

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Hello, world!

Permalink: 2015-11-16 by Daniel S. Standage in blog tags: meta

Seed content for my new notebook.

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